The updated 9 speed in the 2019 Pilot is having significantly less problems than the 2016-2018 Pilot. It is smoother, too.
A minivan will almost always be more practical than an SUV. They are more spacious in the cargo and passenger areas. However, a minivan seems like overkill for two people. Switching from an Odyssey to an SUV is big. You will notice the backseat is a penalty box most of the time. Your Odyssey has a much more comfortable 3rd row than most SUVs. The CX-9 and Atlas are completely different-feeling SUVs that compete in the same class.
Addressing the problems with the CX-9: The rust was a problem with Mazda model years from the early 2000s to about 2010. Rust problems are about as common as any of the other brands now. I have not heard of the weak A/C or especially broken tie rods. There were problems with the infotainment system. If it wasn't fixed with a software update, they usually replace the system. This was a problems with the 2016 model year, but the recent ones seem to have much less issues. Because of this, I would avoid the 2016s.
The CX-9 is definitely one of the more reliable 3 row SUVs. Unfotunately, the 3rd row in the Mazda is virtually useless. They went with a small interior to improve the styling. I like almost everything else about the CX-9, though roominess is one of the most important features in an SUV. It is much more fun to drive than its competition and handles almost like a sedan.
I have driven an Atlas and I really didn't like it. Maybe it is because the only big car I am used to driving is a 2002 Odyssey, which feels much lighter. The Atlas just feels too big. It is heavy, so the engine feels underpowered and the handling is like a boat. Maybe of more importance: the interior does feel almost as large as a minivan. The Virtual Cockpit is nice. The interior feels worse than some modern GM SUVs, which is bad and unusual in a VW.I wish VW made it feel more German and not American.You get poor German reliability with American cheapness in my opinion. Consumer Reports gives the Atlas a Poor reliability rating.
There are many other good SUVs to look at, such as the Kia Sorento, Toyota Highlander, the new Hyundai Santa Fe 2 row, and 2019 Honda Pilot. The Acura RDX is having problems, but is otherwise a great SUV.
I'm not a fan of SUVs and probably will never buy one because you don't get as much car for the money and everybody "needs one" now, so I like the idea of a Genesis G80. It is a good car. I have heard there are some problems with the dealers right now and something about an inventory issue. You buy them through your Hyundai dealer. Depreciation is a problem with Genesis. I feel like a Honda Accord Touring 2.0T would be a little better. It feels very premium, spacious, and drives great. When deciding which rear seat is the best in every auto show I have been to in the past few years, I always think the Accord and Civic are the best. Genesis is in the top five. Cadillac was comfortable, also. The Accord and Civic have heated rear seats in the Touring trim. Accord has heated and cooled front seats.
Feel free to ask more questions and please tell us what you buy!